January 17, 2013

Deep mtDNA substructure in southern Africa (Barbieri et al. 2013)

The Khoisan have been used in many different ways in reconstructions of human history.

Being probably the most genetically diverse modern human population, they are occasionally viewed as akin to the ur-humans, with everyone else shedding diversity via founder effects as they moved away from a south African modern human urheimat.

They are also sometimes viewed as a basal branch of the human family tree, and they probably are -if modern humans are made to fit a tree model. But, modern humans didn't really evolve tree-like (some African farmers have Khoisan-like admixture, and the Khoisan themselves have relatively "shallow" common ancestry with other Africans and many Eurasians on account of their possession of a respectable frequency of Y-haplogroup E).

I have sometimes noted that in the case of South African groups were are lucky that the Khoisan exist as a discrete set of populations, making it easier to discern the legacy of South African hunter-gatherers in the genomes of immigrant farmers and pastoralists who converged southwards over the last few thousand years. This can be contrasted with the presumable situation in places like West Africa (the cradle of Sub-Saharan African farming), in which any indigenous hunter-gatherer groups have ceased to exist as distinct entities a long time ago.

A new AJHG paper sample south African genomes extensively and arrives at a startling conclusion. In the words of the authors:

Overall, the results of this analysis indicate that it is very unlikely that the highly divergent L0k1b/L0k2 lineages were incorporated into the Bantu-speaking populations via gene flow from a population that was ancestral to a Khoisan population in our sample but subsequently lost from the Khoisan population via drift. Instead, these results support the hypothesis that the ancestors of the Bantu-speaking populations carrying the divergent L0k lineages (who now live mainly in Zambia) experienced gene flow from a pre-Bantu population that is nowadays extinct. Alternatively, it is possible that descendants from this pre-Bantu population do exist but have not yet been included in population genetic studies; however, our extensive sampling of populations from Botswana, Namibia, andWest Zambia (which includes representatives of nearly all known Khoisan groups) makes it highly unlikely that this pre-Bantu Khoisan population has not yet been sampled.

In other words, we must resist the tendency to think of the Khoisan as representatives of all pre-Bantu south Africans. The Khoisan are certainly descendants of old south Africans, and represent a part of the pre-Bantu genetic landscape that retained its cultural distinctiveness (and hence can be nowadays sampled as a distinct population). But, there were other, now submerged, peaks in that landscape that are no longer extant in distinct form, but only in absorbed form in the gene pool of south African farmers.

This is fairly interesting in itself, and certainly ought to change our belief about what Africa looked like pre-Bantu expansion. We ought to think of, perhaps, a cornucopia of groups: many of them may have gone extinct; some may have been completely absorbed into more successful ones, and perhaps only a handful survive as distinct entities. Such a view would agree with the conclusions of physical anthropology about the persistence of archaic-leaning groups in parts of Africa down to the Holocene boundary.

The American Journal of Human Genetics, 17 January 2013 doi:10.1016/j.ajhg.2012.12.010

Ancient Substructure in Early mtDNA Lineages of Southern Africa

Chiara Barbieri et al.

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.

13 comments:

Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.

Today, there are no Khoisan speakers, and no hunter-gatherers, in Zambia, as all of its population is Bantu-speaking, and agriculturalist traditionally. Thus within the territory of Zambia, whatever genetic legacy of the pre-Bantu population there remains today is totally ingrained within the DNA of its Bantu population. How much pre-Bantu DNA do modern-day Zambians have, and how similar is it to the genetics of the Khoisan peoples? We do not know, as, to my knowledge, there is yet no study dealing with the autosomal genetics of Zambians. I bet that the pre-Bantu genes of Zambians will turn out to be very Khoisan-like when studied. That the sublineages L0k1b and L0k2 are possibly not found in the modern-day Khoisan peoples does not mean much, as today's Khoisan peoples are a genetically bottlenecked and geographically much shrinked human population as a result of the Bantu expansion.

In addition to the extant several Paleo-African populations of Africa (Bushmen, two groups of Pygmies and in Tanzania), there was already another extinct modern human Paleo-African population disclosed by genetic studies in admixture remnants in Mozambique. So the evidence of an extinct Paleo-African population in Southern African in addition to the Khoisan isn't so surprising.

It would be worth going back to the Mozambique paper, however, to see if this extinct South African population is the same, or different from the one seen as a substrate layer in Mozambique.

"Put the pieces together and one can imagine as of ca. 16,000 years ago (within a few millenia of the population of the Americas by modern humans), an ancestral West African population, two ancestral East African populations in addition to the Hadza, an ancestral Mozamibiquan population, an ancestral Khoisan population, an ancestral Eastern Pygmy population, an ancestral Western Pygmy population, and an ancestral North African population that has left behind few discernable traces and was soon to be demographically overwhelmed by West Eurasian back migration even if they have left some residual genetic traces in the modern residents of North Africa."

There may have been at least one more ancestral South African population to add to the list.

Re: Mozambique autosomal genetics the source is a 2010 article in the European Journal of Human Genetics (open access, citiations omitted):

"The southeastern Bantu from Mozambique are remarkably differentiated from the western Niger-Congo speaking populations, such as the Mandenka and the Yoruba, and also differentiated from geographically closer Eastern Bantu samples, such as Luhya.

These results suggest that the Bantu expansion of languages, which started ~5000 years ago at the present day border region of Nigeria and Cameroon, and was probably related to the spread of agriculture and the emergence of iron technology, was not a demographic homogeneous migration with population replacement in the southernmost part of the continent, but acquired more divergence, likely because of the integration of pre-Bantu people.

The complexity of the expansion of Bantu languages to the south (with an eastern and a western route), might have produced differential degrees of assimilation of previous populations of hunter gatherers. This assimilation has been detected through uniparental markers because of the genetic comparison of nowadays hunter gatherers (Pygmies and Khoisan) with Bantu speaker agriculturalists.

Nonetheless, the singularity of the southeastern population of Mozambique (poorly related to present Khoisan) could be attributed to a complete assimilation of ancient genetically differentiated populations (presently unknown) by Bantu speakers in southeastern Africa, without leaving any pre-Bantu population in the area to compare with. . . the fact that our dataset of 2841 SNPs has only limited fine-scale resolution makes the observed strong differentiation of the population from Mozambique even more striking." It appears that the Mozamibique population was an L1d population.

We just recently started an L0 haplogroup project at FTDNA, and anyone who has tested as L0 is welcome to join the project (or email me results from 23andMe). I recently downloaded the 48 available L0d and L0k FMS sequences, so this study will increase the available FMS samples for those haplogroups by a factor of 10.

I much prefer the way you put it Dienekes "no longer extant in distinct form, but only in absorbed form in the gene pool of south African farmers" instead of extinc. There was obviously admixture, therefore these populations are descentants of these populations, therefore not extinct.

@andrew: As I noted a while back, the Italian traveller Ludovico di Varthema seems to have encountered click speakers when he visited Moçambique around 1505:

We found some races of people quite black and quite naked, excepting that the men wore their natural parts in a bark of wood, and the women wore a leaf before and one behind. These people have their hair bristling up and short, the lips of the mouth as thick as two fingers, the face large, the teeth large and as white as snow. They are very timid, especially when they see armed men.

[...] we descended on the other side and found some caverns, to which the said negroes resorted, who speak in a manner I shall have great trouble making you understand. However, I will endeavor to explain it to you in the best way I can. For example: when the muleteers follow their mules in Sicily and wish to drive them on, with the tongue under the palate they make a certain warble and a certain noise, with which they make the mules go on. So is the manner of speaking of this people, and with signs until they are understood.

Interestingly, they are described as being food producers in possession of cattle.

"That the sublineages L0k1b and L0k2 are possibly not found in the modern-day Khoisan peoples does not mean much, as today's Khoisan peoples are a genetically bottlenecked and geographically much shrinked human population as a result of the Bantu expansion. "

Yes, and bottlenecking is only part of the answerr. Why would the "Khoisan" population have to be any more related than the supposed Khoisan languages are? THe more people look at them, the less related they seem to be.

As I understand the matter, some of the Bantu languages in parts of Mozambique, via substrate influence for the languages spoken before they experienced language shift, retained the click phonemes even through they are not Khoisan languages. So, the presence of clicks in 1505 does not definitively establish that a Khoisan rather than a Bantu language was being spoken.

I am not familiar enough with the modern day residents of the region to know how much of a typically Khoisan as opposed to a typical East or West African Bantu physical appearance is discernable among speakers of the Bantu click languages. If people with that physical appearance no longer live there, the physical anthropology is probably more probabitive of the Khoisan v. Bantu click language question than the use of clicks alone and may support your conclusion.

"some of the Bantu languages in parts of Mozambique, via substrate influence for the languages spoken before they experienced language shift, retained the click phonemes even through they are not Khoisan languages".

And in South Africa. Xhosa for example is a 'click' language.

http://en.wikipedia.org/wiki/Xhosa_language

So as well as pre-Bantu haplogroups surviving in southern Africa we have elements of the language in the form of clicks surviving.

I think this is potentially significant as the Bantu expansion from one very specific region by a population with their own very specific population history may have overwritten other populations who were critical in the out of Africa process i.e. there could have been stages of cultural or physical evolution in a sequence moving away from the tropics which were the foundations of the later move i.e. the people who made the move were different to the Bantu who came after.

The really interesting thing about di Varthema's account is that his mountainous landscape of caves is situated in the mainland opposite Ilha de Moçambique, in the northern part of the country. No Bantu languages possessing click phonemes, my sources tell me, are today attested beyond southeast Mozambique (see the transposed maps in my earlier link). But yes, you're correct in that the linguistic coherency of "Khoisan" is seriously doubtful and that non-Bantu click-speakers as a whole are genetically disparate (as can be seen in comparisons of Sandawe and the southerly bushmen).

"Khoisan" physical features are fairly evident in various South African Bantu peoples (see, e.g., Nelson Mandela, a Xhosa). Can't say whether there's any vestige of this in northern Mozambique, but H.H. Johnston claimed the persistence of folk memories of such people amongst Bantus residing further inland along this latitude: a dwarfish, yellow-skinned, click-using, stone-throwing people on the tops of certain high mountains.

Maju at his blog notes that there are some representatives of mtDNA haplogroups closely related these in Kuwait and Yemen respectively, although the frequency is quite low and one could imagine mechanisms such the Indian Ocean trade (either voluntary or slave trade) producing these outliers.

Andrew. Maju insists they are remnants of the single original OoA but I agree that the presence is most probably explained by the Indian Ocean trade. I have had many bitter arguments with him on the subject.

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